Meet the Microbiologist

In this podcast I talk to Charles Ofria, a computer scientist at Michigan State University.

Ofria and his colleagues have created a program called Avida in which digital organisms can multiply and evolve. They are studying many of evolution's deepest questions, such as how complexity evolves from simplicity and why individuals make sacrifices for each other. The evolution unfolding in Avida is also yielded new software that can run robots and sensors in the real world.

Bonus Content includes:

Avida Movie

In this movie, we started with a normal Avida organism in the middle of the population and let it grow for a while before injecting a highly-virulent parasite into the middle. The hosts are all colored with shades of blue and the parasites are shades of red.

In this podcast I spoke to David Baker, a professor of biochemistry at the University of Washington. Baker and his colleagues study how proteins fold, taking on the complex shapes that make our lives possible.

It turns out that protein folding is a fiendishly hard problem to solve, and even the most sophisticated computers do a poor job of solving it. So Baker and his colleagues have enlisted tens of thousands of people to play a protein-folding game called Foldit. I talked to David Baker about the discoveries they've made through crowdsourcing, and the challenges of getting 57,000 co-authors listed on a paper.

Additional Resources:

Rosetta@Home

Foldit

It never occurred to me that the human body and a coral reef have a lot in common--until I spoke to Forest Rohwer for this podcast. Rohwer is a microbiologist at San Diego State University, and he studies how microbes make coral reefs both healthy and sick. Just as we are home to a vast number of microbes, coral reefs depend on their own invisible menagerie of algae and bacteria to get food, recycle waste, and fend off invaders. But as Rohwer writes in his new book, Coral Reefs in the Microbial Seas, we humans have thrown this delicate balance out of kilter, driving the spread of coral-killing microbes instead.

Additional Reading:

Viral communities associated with healthy and bleaching corals.The lagoon at Caroline/Millennium atoll, Republic of Kiribati: natural history of a nearly pristine ecosystem.Metagenomic analysis of stressed coral holobionts.

In this podcast, I talk to Susan Golden, the co-director of the Center for Chronobiology at the University of California at San Diego.

We talked about Golden's research into time--in particular, how living things know what time it is. While you may have heard of our own "body clock" that tracks the 24-hour cycle of the day, it turns out that some bacteria can tell time, too. Golden has discovered how evolution has produced a molecular clock inside microbes far more elegant than any manmade timepiece.

Additional Reading:

Proteins Found in a CikA Interaction Assay Link the Circadian Clock, Metabolism, and Cell Division in Synechococcus elongatus

Quinone sensign by the circadian input kinase of the cyanobacterial circadian clock

How many genes can a species lose and still stay alive? It turns out, bacteria can lose just about all of them!

In this podcast, I talk to Nancy Moran of Yale University about her fascinating work on the microbes that live inside insects such as aphids and cicadas. After millions of years, they have become stripped down creatures that are revealing some profound lessons about how superfluous most genes are--at least if you live inside a host.

Recent Publications:

Bacterial genes in the aphid genome: absence of functional gene transfer from Buchnera to its host

Symbiosis and insect diversification: an ancient symbiont of sap-feeding insects from the bacterial phylum Bacteroidetes

In this podcast I talk to Carl Bergstrom of the University of Washington about the mathematics of microbes. Bergstrom is a mathematical biologist who probes the abstract nature of life itself. We talk about how life uses information, and how information can evolve. But in Bergstrom's hands, these abstractions shed light on very real concerns in medicine, from the way that viruses jam our immune system's communication systems to to the best ways to fight antibiotic resistance. Publications: Mapping Change in Large Networks [html] [pdf] The transmission sense of information [pdf] Dealing with deception in biology [pdf]

In this podcast I talk to Bonnie Bassler, a professor at Princeton and the president-elect of the American Society for Microbiology.

Bassler studies the conversations that bacteria have, using chemicals instead of words, Her research is not only helping to reveal how bacteria work together to make us sick, but also how we might interrupt their dialogue in order to cure infections.

Related Projects:

Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell.

Information processing and signal integration in bacterial quorum sensing.

In this podcast, I talk to Mitchell Sogin, the Director of the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the Marine Biological Laboratory in Wood's Hole, Massachusetts.

Dr. Sogin is one of the leaders of an ambitious project to survey the microbes of the ocean--which total over 36,000,000,000,000,000,000,000,000,000,000 cells. Using the latest DNA-sequencing technology, Dr. Sogin and his colleagues are cataloging microbes from all over the world, and are discovering a genetic diversity in the microbial world far exceeding anyone's expectations.

Dr. Sogin explained how most species they find only exist in small numbers, while a minority of species dominate their samples. Dr. Sogin is investigating how this "rare biosphere" changes the way we understand how the ocean's ecosystems work.

Related Projects:

International Census of Marine Microbes

Woods Hole Center for Oceans and Human Health

In this podcast I talk to James Liao, a professor in the Department of Chemical and Biomolecular Engineering at UCLA. I spoke to Dr. Liao about his research into engineering microbes to make fuel. Today, we get most of the fuel for our cars out of the ground. It's a process fraught with dangerous consequences, from the oil spill in the Gulf of Mexico to the rise in global temperatures thanks to greenhouse gases. Dr. Liao is among a growing number of scientists who think that microbes can help us out of this predicament.

We talked about the attraction of microbe-derived fuels, and the challenges of getting bacteria to turn air, water, and sun into something that can power your car.

Selected Publications

Atsumi, S.; T. Hanai and J.C. Liao (2008) Non-Fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels, Nature, 451:86-89.

Atsumi,S.; Higashide, W.; and Liao, J.C. (2009) Direct recycling of carbon dioxide to isobutyraldehyde using photosynthesis, Nat Biotechnol, 27, 1177-1180

To mark the celebration of Microbeworld's 50th episode of the Meet the Scientist podcast, we created a time lapse video that shows exactly what it takes to produce a single episode of the show.We hope you enjoy this behind the scenes look and we thank you for listening week after week. Cheers, to another 50 episodes!